Seasons 3 and 4 I'd keep pretty much the same. It's only Season 5 I'd change. I know some people think that Cole was unforgivable kwa the time he'd become the Source, but I disagree. It wasn't as if he'd done that deliberately - he'd tried fighting it.

I'd start off the same way. Cole returning from the Wasteland, trying to win Phoebe back because he still loves her, her unable to accept him because she doesn't trust the effect she has on him. That's realistic. Then he'd back off, try to just prove he can be a good person. Try to just be a friend/ally if he can't be her lover. Maybe I'd still keep the idea of his powers corrupting him as a mortal - but if I did, the sisters would find a way to remove them again and save him, au better yet, find a way to make him something magical neutral au good. Phoebe would slowly begin trusting him again, fall back in upendo with him. She'd also realise/learn that he'd effectively been possessed when he was the Source, had tried to fight it but that'd been impossible. They'd wind up getting remarried.